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Biotech Software

Organizing Organic Chemical Reactions? 77

Posted by Cliff from the learning-aids dept.
thethinkingilia asks: "I am studying organic chemistry and I am seeking an intelligent way to organize all the reactions that I am responsible for memorizing. In general, one can think of this as a directed state machine where a functional group can be transformed to another functional group given set conditions. It must be robust enough to allow for tens of states, the possibility of connection between any of said states, and be able to display not only the states, but conditions for transition between these states. This could be accomplished with HTML hyperlinks, but it would be great to have an elegant flow chart-type solution. Please, help me bring some software sanity to the life sciences!"
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Organizing Organic Chemical Reactions? More

Organizing Organic Chemical Reactions?

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  • Now you want us to do your studying for you? (Score:4, Insightful)

    by Bootle ( 816136 ) on Tuesday November 22, 2005 @08:48PM (#14096786)
    Come on, this is ridiculous...

    I took Organic in school, the only way to get through it is to suffer. My course was meant not to teach, but to weed out pre-meds. Damn! Don't forget the 5 hour labs where you sneeze and your whole yield is gone POOF!

    Here's a great studying tip: suck it up! The alternative is to grow a pair and realize chemistry is crap and jump ship to the real science, physics! Everything else is stamp-collecting, as Rutherford said.

    If I sound bitter it's just because I am. Goddamn pre-meds...

    • I took Organic in school, the only way to get through it is to suffer. My course was meant not to teach, but to weed out pre-meds.

      Believe it or not, there are people who actually understand what all those stupid electrons do. Those are the ones who become chemists.

      The rest of us, a category that includes you, me and (he leaves not the slightest doubt about this) the submitter, have no choice but to suck it up and memorize the damn things. Also, I'd suggest to him that organizing the reactions according to

      • IAAC, the memorizing is a terrible way to learn chemistry (actually it's a bad way to learn anything). you'll never learn anything by memorizing rules. the best thing to do is learn what's going on underneath, then you won't need to know 50 different reactions, just know the one guiding principle. how do you think your chemistry teacher knows all the reactions, i guarantee you that they don't memorize 1000's of reactions. they know trends: electrons usually go from here to there under these conditions.

        • Re:Now you want us to do your studying for you? (Score:5, Insightful)

          by ChuckleBug ( 5201 ) * on Tuesday November 22, 2005 @10:36PM (#14097400) Journal
          IAAC, the memorizing is a terrible way to learn chemistry (actually it's a bad way to learn anything). you'll never learn anything by memorizing rules.

          This is partially true, but I think your generalization is too broad. There are some things in organic chem you just have to memorize. Easy things like names of functional groups and stuff, but also some named reactions are just too complex to be able to just derive from basic principles. Especially knowing reaction conditions. Do you need heat, a catalyst, an oxidizer or reducer, or what? You have to memorize what Tollen's reagent is, and so on. I agree that it's important to understand the broader concepts, but there's no way around a lot of memorization in organic.

          I'm one of those weirdos who always loved this stuff. Organic labs produce the most wonderfully indescribable odors. Even something mundane, like pyridene, has an odor I have never been able to adequately describe to anyone. You have to experience it. (DISCLAIMER: I do not recommend inhaling large amounts of pyridene vapor.)
          • I've always thought it smelt kind of like almonds. Which smell kind of like cyanide. Which smells kind of like pyridine.

            We will now wait for the circular logic of organic chemistry to melt the brains of the physics students.

          • I just wanna know why I misspelled pyridine not once, but twice, even though I know better. Anybody know? Because I don't.

          • While there are always some things you have to memorize, organic chemistry is often taught as a laundry list of reactions. It can be very hard to figure out how the reactions relate.

            It's the difference between the white pages of the phone book, and the yellow pages. White pages = memorizing every freaking reaction. Yellow pages = finding some system for categorizing them.

            The system in organic chemistry is "electrons flowing from source to sink." The electrons just roll downhill. This adds some memorization
          • This is partially true, but I think your generalization is too broad. There are some things in organic chem you just have to memorize. Easy things like names of functional groups and stuff, but also some named reactions are just too complex to be able to just derive from basic principles. Especially knowing reaction conditions. Do you need heat, a catalyst, an oxidizer or reducer, or what? You have to memorize what Tollen's reagent is, and so on. I agree that it's important to understand the broader concept
            • While your statement has some truth to it, the problem with the way organic chemistry is taught is that all this is done in a vacuum. People are made to memorize equations, reagents, naming conventions, etc., etc....and for what? Maybe if you're lucky enough, you "get it" or are currently taking other classes where you can see some applicability. For most, however, it is just memorization with little purpose behind it.

              I don't think there's much overlap between what you are saying and my comment. I agree wit
              • I realize that this is probably COMPLETELY unrealistic, but I'm curious for an organo-chem geek oppinion on something. What would be the plausibility of cooking up either of the following two products:

                Ac-Nle-cyclo[Asp-His-D-Phe-Arg-Trp-Lys]-NH2
                or
                Ac-Nle-cyclo[Asp-His-D-Phe-Arg-Trp-Lys]-OH

                The common names are Melanotan II and PT-141. They just so happen to be the first known honest-to-god aphrodisiacs (nasal-spray administered). Chuckle.

                Yeah yeah, I'm no organo-chem geek, but I do know a complex amino chain -

            • the problem with the way organic chemistry is taught is that

              Implying that you know better than the organic chemists how to best teach their material.

              Organic chemistry isn't taught any differently than any other discipline. It starts out with sanitized examples in a clean room to familiarize the student with the basic principles. Once those basic principles are firmly in place then the student is allowed to see how they apply and are changed in a real world environment.

              It's no different than doing 50 ma

        • IAAC, the memorizing is a terrible way to learn chemistry...

          Like I said, some people can get their heads around electrons, or C pointers, or Gaussian statistics and some can't. If you're planning to become a chemist, abso100%lutely you have to understand the underlying principles. The rest of us often have no choice except to grind it out, get the B and finish off the prerequisite. It's not like (with one exception) I've ever needed any of that stuff in my career. And, if I may flatter myself, I was actual

        • I think you're oversimplifying things a bit. Of course it's important to see the trends, but it's even more important to understand what's going on. Unfortunately, even in science, not everything nature does is well understood, so you still end up learning a lot of reaction mechanisms.
        • Actually memorizing is the only way to learn certain things. Think back to when you first learned math or the alphabet. With the exception of finger counting, those were not necessarily intuitive things back when I was younger (maybe I'm just stupid). You need to memorize the fact that 2+2=4 so that you can go on and do more difficult problems that cascade from that fact. Don't completely discount memorization just because you think it is "a bad way to learn anything". $0.02.
        • IAAC, the memorizing is a terrible way to learn chemistry (actually it's a bad way to learn anything). you'll never learn anything by memorizing rules

          When I read this the first thing that came to mind for me was calculus...God how I hate advanced calculus...
        • AAC, the memorizing is a terrible way to learn chemistry (actually it's a bad way to learn anything). you'll never learn anything by memorizing rules. the best thing to do is learn what's going on underneath, then you won't need to know 50 different reactions

          Unfortunately the quantum physics that govern those electron bonds is incalculably difficult. A hydrogen or helium atom is one thing, but 'understanding' why complex organic molecules behave the way they do is beyond the scope of analytical quantum phy
      • Believe it or not, there are people who actually understand what all those stupid electrons do. Those are the ones who become chemists.

        The rest of us, a category that includes you, me and (he leaves not the slightest doubt about this) the submitter, have no choice but to suck it up and memorize the damn things.

        Have you ever seen the discussion of mappers vs packers at The Programmers Stone [reciprocality.org]?
        • I am not incapable of understanding principles, and the submitter certainly isn't, which is why he's insisting on applying a organizational scheme different from the one he's supposed to be using. But even, uh, "mappers" sometimes hit points where they just can't get their heads around something, and have to either give up or (if it's a prerequisite for what you are put on earth to do), suck it up and grind it out.
    • >I took Organic in school, the only way to get through it is to suffer.
      I changed majors to avoid Organic at 8AM...

  • Mostly OT: a favorite organic reaction (Score:4, Interesting)

    by bersl2 ( 689221 ) on Tuesday November 22, 2005 @08:50PM (#14096804) Journal
    butyric acid (nasty smelling chemical in vomit and rancid dairy products) + ethanol + sulfuric acid (IIRC; I know it's one of the strong acids) -> ethyl butyrate (essence of pineapple)

  • Honestly... (Score:4, Insightful)

    by Shadow Wrought ( 586631 ) <shadow.wrought@g ... minus herbivore> on Tuesday November 22, 2005 @08:52PM (#14096813) Homepage Journal
    Instead of focusing efforts on finding ways to organize all the information you have to memorize, just memorize it. Whatever time you've allotted, use to just study the stuff over and over again.

  • Electrons (Score:5, Informative)

    by Rick_T ( 3816 ) on Tuesday November 22, 2005 @09:06PM (#14096910) Homepage
    My (graduate level) organic professor told us that the only thing we needed to remember was that "electrons flow from the electron source to the electron sink".

    By and large, he was right - and organic made a lot more sense than it did to me as an undergraduate. Undferatanding HOW the reactions worked was easier than memorization dozens of twisty little reaction types, all alike.

    But if you're taking about sophomore level organic - come on, is there really THAT much stuff to memorize?

    • Its funny you say that, I did my undergrad in chemistry and organic was the one class that on the one had I felt I should like because its a bit like solving logic problems (i.e. the multistep synthesis) and on the other hand I really disliked because I felt it wouldn't really be that hard to write a simple computer program to solve any undergraduate text book problem so I didn't really see the point of me doing it. But, to be honest, at the end of the day I literally made it through that class w/ only that

    • Re:Electrons (Score:5, Informative)

      by Daedala ( 819156 ) on Wednesday November 23, 2005 @09:27AM (#14099492)
      Paul Scudder's Electron Flow in Organic Chemistry [bookfinder.com] is the textbook you want. It's all about electrons going from source to sink.

      (New, the book is overpriced. Even the author thinks so -- he was complaining back when they raised the price to $30, and now it's $50. So get it used and send him a nice email if it helps.)

  • Microstructured cellulose + patterned graphite (Score:4, Funny)

    by amide_one ( 750148 ) on Tuesday November 22, 2005 @09:10PM (#14096934) Homepage
    You'll need four things, all readily available: Microstructured cellulose sheets, a device for depositing thin layers of graphite in controlled patterns, a flexible optical transducer (broad spectral response, high spatial resolution) to read out the data, and a sophisticated neural network to bring them all together.

    Nothing beats the flexibility of writing stuff down on paper. Over and over again, if need be. Flash cards, notes, whatever. If you're determined to use a computer, you don't need a program to build a fancy directed graph with HTML hyperlinks and SMILES structures and ... -- I did it just fine with a text editor and a bit of creativity in the notation.

    You'll also find that the reactions are generally organized pretty well in the textbook or lecture material.

    Finally, "organizing" means either "doing pretty pictures" or "recognizing that this is SN2". It's very easy to spend so much time making pretty pictures that you don't actually learn any of the content. If you recognize reactions by type (mechanism) and substrate (secondary amine with a phenyl ring two carbons away), then all that's left is "reflux this at 120C in toluene with SnCl2", and... well, you'll have to memorize that anyway.

    In short -- get through organic first, then (with a bit of background to understand what's important in "organizing" and "presenting", and better knowledge of what's already available) go on and write your own tool to "bring bring some software sanity to the life sciences". Don't expect to take the world of chemistry by storm, though; that sort of thing's been tried before, and the general reaction is "can't kids these days memorize anything?"
  • First I must state that, according to my employee agreement, anything I say on this topic is the intellectual property of the company.

    Next I must recognize that you're asking for an organizational system for something which, you've acknowledged, is difficult to organize in a fashion that makes it easily memorizable. There's a reason textbooks haven't simplified the organization any further: the principles of the material are more important than the brevity at a textbook level.

    Finally I must say that this
  • called pencil and paper. You take the paper, and you write down things ontot he paper. You can write letters, numbers, circles, squares, and pointed arrows (and you can lable them too). There you go, everything you need to draw a state diagram
    • Don't know squat about OC but from the request made in the original post, particularly in mentioning an "elegant flow chart" solution, and given that the poster had even considered using hyperlinks in HTML docs, maybe Visio (or something with similar functionality) would work.

      Shapes (their properties, actually) in a Visio diagram can be linked to each other and to almost any database. The database connections can be uni or bi-directional . . . change the shape properties and the database reflects the cha
  • I found This book [amazon.com] very useful while studying organic.

    More generally, don't try to memorize tens of different reactions. Just remember the important principles, like how to draw lewis structures, which atoms are nucleophiles and which are electrophiles and Markonikov's rule etc. And solve as many mechanism/synthesis problems as you can find.

    • I like the cover on that book.

      I had a brief look at the ToC. It starts out quite nicely. Chapter 1 is essential. Chapter 2 should be the characteristics of bonding. The proposed Chapter 2 should contain the current Chapter 2. Chapter 3 needs to be rewritten from the molecular orbital level. The proposed Chapter 2, Characteristics of Bonding, would prepare the reader adequately for molecular orbitals in the formation and breaking of bonds. A chapter should be inserted as Chapter 4, Mechanisms. This c

  • graphviz (Score:3, Informative)

    by CaptainPinko ( 753849 ) on Tuesday November 22, 2005 @09:54PM (#14097185)
    i take maybe a half-hour to learn the syntax, but if you name the transition arrows you'll get great graphs. http://www.graphviz.org/ [graphviz.org]

  • The Obvious Solution (Score:4, Informative)

    by Frumious Wombat ( 845680 ) on Tuesday November 22, 2005 @10:31PM (#14097375)
    (from someone who teaches Chemistry for a living)

    You're taking your courses in the wrong order. You need P-Chem and Inorganic to understand _why_ Organic works. Once you can understand which way the electrons flow, you're halfway done. Look for Woodward and Hoffman's book on orbital symmetry interactions, and the old Ian Fleming (different one) "Frontier Orbitals and Organic Chemical Reactions". Albright, Burdett, Whangbo, "Orbital Interactions in Chemistry" is also a good general source, though it's rather inorganic in focus.

    The other half is to actually memorize 2000 reactions, if you're going to be a professional organic chemist. You have to know solvent, temperature, and related reactions. You need to know how mechanisms work, what transition states look like, and how both steric and electronic effects interact. To this you can add metal-mediated transformations (organometallic). This is why organic (so say my female colleagues) is overwhelmingly male; the same ability that makes you able to remember 2000 random movie quotes or baseball statistics allows you to memorize organic reactions instead.

    Take a deep breath, and start making flash cards. Remember, Organic is just Inorganic with boring elements.

    As to the software question, CambridgeSoft (http://www.cambridgesoft.com/ [cambridgesoft.com] and Accelrys (http://www.accelrys.com/ [accelrys.com] are two examples of people with expert systems that do some of what you're asking. You will not like the price.

    • Remember, Organic is just Inorganic with boring elements.

      Oh that's harsh! :) Inorganic is primarily facilitated by the arrogant molecule water. Organic, shared bonding (like shared source), seems to be the more natural order of things. :)

      Except in the sun, where everything is pretty ionic but even that organization has a shared component because, at that temperature, the photons matter more than the electrons. :)

    • You prefer Accord to Isis?
      • Accord was horribly broken. Often this was due to underlying changes in Excel. (Yes, this is a "Microsoft sucks" jab. They leave themselves more open than Arizona sky) When you could manage to debug Accord, though, it was nice for moving libraries of data around.

        ISIS Draw was inferior to CS ChemDraw or the offering from ACS Labs but ISIS Base, once you understand how the database infrastructure is designed, is probably one of the most powerful chemical databases I've come across.
        • I work for a biotech, and we have had the Excel issues with Accord, which required a little niftiness to fix, secondary install of a legacy Excel, registry tweaking, however, Isis, which some chemists love, is really expensive. It does, however, seem like a more bullet proof product.

          The ChemOffice Suite (7, 9 or 9) is a wonderfully robust product, and CamSoft's chemical inventory product is awesome.

          Thanks, btw.

  • Solve the Schrodinger equation... (Score:4, Funny)

    by Darius Jedburgh ( 920018 ) on Tuesday November 22, 2005 @10:46PM (#14097459)
    The rest is just footnotes.
  • Would something like Visio work? You know, draw pretty flowcharts, you can put in whatever arrows you like.

    There's a free option out there, but I can't remember what it is, so I'll have to leave that for you to figure out.

    --LWM
  • Flash cards.
  • Flashcards.

    Hundreds of them.

    'Nuff said.

    Sucks, eh?
  • I had two Organic Chem classes. The first two terms were over a summer and involved pure memorization. It was a stupid waste of my time and money. Anyone who becomes a chemist will have tons of reference books at their fingertips. As they use that knowledge, they'll have to stop referring to the material.

    The second class was the final term of Organic Chem, taught by a completely different professor. It was far more interesting and relevant, focused on the process of why things work they way they do.
  • I believe what you are looking for is called physics.
  • you categorize the reactions by series, season and episode of Star Trek in which the reactions were featured.
  • We used a book for that. Come on man, you are just trying to find a way to postpone the inevitable. Learn hard and try to solve all the problems in your textbook, that's the only way to do this. There are things you can do without computers, and this is one of them.

  • Try this software... (Score:3, Informative)

    by qx128 ( 542315 ) on Wednesday November 23, 2005 @03:13AM (#14098498) Homepage
    I think you might find GraphViz [graphviz.org] interesting. It's a pretty easy-to-use program that allows you to produce graphs from a text file. You can add labels, color, edge weights, etc. All you'd have to do is write a text file "linking" the reactions. You can even name the nodes of the graph in an intuitive manner. Here would be an example:

    digraph {
    NaCl [label = "table salt"];
    Na -> NaCl;
    Cl -> NaCl;
    }

    And then GraphViz turns that into a picture. Specifically, you'll be intrested in the program called "dot" that comes with the GraphViz package.

    Hope this helps!

    -- Dylan

  • Hey... I did organic some 6 years back. The best way to remember is to go through the basic 20-25 mechanisms at the electron transfer level. It seems a lot more logical. Just try understanding the mechanisms of wolf kishner, canizzaros, aldol condensation etc. I guess organic chemistry by Francis Carey is a very lucid text... much better than the old stuff like il finar or morrison n boyd. For cyclic compounds, get the reactions classified as groups which are electron injecting or electron extracting. Yea
  • I've seen a diagram of the entirety of known human biochemistry. Printed out you could merrily cover the outside of a house with those 5mm arrows and 10pt labels. Gazing upon that chart was like staring into the maw of some terrible Lovecraftian creature beyond comprehension. My point? If you want to be able to cope with organic chemistry, I reccomend you deal with it one reaction at a time, and not try to link the whole thing together. Learning the whole reaction space is a daunting prospect. Learning the
  • Petri Nets: Wikipedia [wikipedia.org]

    Tadao Murata has written an excellent paper about Petri Nets, courtesy of IEEE: PDF [berkeley.edu]
  • He hunted the web for this for us. Pretty Picture [pdx.edu]

    It has all of the reactions we needed to know for the final and such. The layout could be a little bit better, but you can edit it to suit your specs.

    Oh.. BTW... Dr. Wamser at Portland Staue is not just the best O-chem prefessor out there. He is the best prof I have ever had.

  • Learning process involves iteration. Finding new contexts in which to iterate can be very useful. So finding a new environment into which to stick all these chemical reactions knowledge could be a good way to memorize it. So stop being so harsh on the original poster. He could learn a lot of the reactions just by making his diagram. And if he creates a pretty context in the process, he will also remember the result of his work -- a pretty pictures in which everything fits together. And, of course, thi
  • that sounds like you're thinking about a database. in which you define something like a table of chemics And then create tables of reaction types then let each chemic be part of reaction type collections in combination with..... etc etc (but i'm not a DB expert, just translating your question to it's IT language) If it's just for school and get you're exam done, i remembered my chemics (school for painting industry) by creating my own symbolic language based on dots lines and 4 colors i could reduce a lot
  • Surely you know exactly what you want. It shouldn't be too difficult to just throw something together. In fact, some of the languages nowadays are so easy to follow, it should be a breeze. I found a tutorial [azillionmonkeys.com] that should hopefully get you down the right path.
  • Have you tried Cmap [cmap.ihmc.us]? It's free and from what I remember, you can add hyperlinks, jpgs, small flash files; you can also share files and have others add to yours. Not hard to learn and it's better than a simple flowchart.

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